The two-leg semi-final finished 1-1 on aggregate after a goalless match in Algiers last weekend.
USM now face Zamalek of Egypt on May 9 and 16 in the final.
At stake in the African equivalent of the UEFA Europa League will be a record $4 million first prize - an increase of 100 percent from last season.
The kick-off was delayed 80 minutes after rival supporters threw projectiles and a Moroccan journalist was reportedly taken to hospital having been assaulted.
Ahmed Khaldi converted a penalty four minutes into first half added time to put the Algiers outfit ahead and leave Safi needing to score two unanswered goals to reach the final.
They managed one, after 75 minutes, when Senegalese substitute Moussa Kone scored his sixth goal of the African campaign with a far-post header after a corner.
But the home team, roared on by the majority of supporters in an 8,000-capacity stadium in the southern coastal city, rarely looked like scoring again.
After 10 minutes of added time in the first half, an additional 20 minutes were added to the second period in a tense match that was constantly interrupted.
Players feigned injuries and constantly disputed decisions of the Rwandan referee, bottles were flung on the pitch and fireworks temporarily created a cloud of smoke over the pitch.
USM won the Confederation Cup in 2023 and claimed a second CAF trophy that year thanks to a surprise victory over then African champions Al Ahly of Egypt in the Super Cup match.
Zamalek are the second most successful club in CAF competitions after Cairo neighbours Ahly, winning 13 titles, including the Confederation Cup twice.